BioProject

DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. More...

DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. We demonstrated that NT-seq reliably detects three types of methylation motifs in E. coli and H. pylori genomes. We further applied NT-seq to a microbial community standard for de novo methylation motif discovery. Finally, by coupling methyl DNA immunoprecipitation and NT-seq (DIP-NT-seq), we showed that 6mA could be accurately mapped at single-base resolution in the bacterial and eukaryotic genomes. NT-seq thus provides a simple and reliable solution for detecting multiple types of DNA methylations. Overall design: NT-seq in both native and amplified DNA after 6mA DIP enrichment Less...